In plant and animal breeding studies a distinction is made between the genetic value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this paper, we argue that t…
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48 results for “Genetic effects”
Efficiently infers graph edges from genetic similarity data in landscape genetics.
problem Inferring unknown graph edges from genetic similarity data in a heterogeneous landscape.
method Developed an efficient first-order optimization method to solve the inverse landscape genetics problem.
result Our method provides fast and reliable convergence, significantly outperforming existing heuristics.
Genome-wide association studies (GWAS) have emerged as a rich source of genetic clues into disease biology, and they have revealed strong genetic correlations among many diseases and traits. Some of these genetic correlations may reflect causal relationships. We developed a method to quantify causal relationships betwe…
Locally epistatic genomic relationship matrices for genomic association, prediction and selectionstat.AP
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our aims include reducing the dimensionality of the problem that has to be dealt one a…
BayesMR estimates causal effects and directionality from genetic data.
problem Challenges in finding good genetic instruments and estimating causal effects.
method Bayesian Mendelian randomization approach that accounts for pleiotropy and reverse causation.
result BayesMR provides a posterior distribution over causal effects and uncertainty.
Deep models improve GWAS by identifying genetic interactions.
problem Missing non-linear interaction effects in GWAS.
method Gradient-based DeepLIFT technique to interpret deep models.
result Known and novel genetic risk factors identified.
ENN method uses expectile regression for genetic data analysis of complex diseases.
problem Discover additional genetic variants contributing to complex diseases.
method Developed an expectile neural network (ENN) method integrating expectile regression and neural networks.
result ENN method outperforms existing expectile regression in discovering genetic variants predisposing to sub-populations.
Genetic algorithms have been widely used in many practical optimization problems. Inspired by natural selection, operators, including mutation, crossover and selection, provide effective heuristics for search and black-box optimization. However, they have not been shown useful for deep reinforcement learning, possibly …
We introduce the Genetic-Gated Networks (G2Ns), simple neural networks that combine a gate vector composed of binary genetic genes in the hidden layer(s) of networks. Our method can take both advantages of gradient-free optimization and gradient-based optimization methods, of which the former is effective for problems …
Genome-wide association studies (GWAS) have achieved great success in the genetic study of Alzheimer's disease (AD). Collaborative imaging genetics studies across different research institutions show the effectiveness of detecting genetic risk factors. However, the high dimensionality of GWAS data poses significant cha…
Identifying Outliers using Influence Function of Multiple Kernel Canonical Correlation Analysisstat.ML
Imaging genetic research has essentially focused on discovering unique and co-association effects, but typically ignoring to identify outliers or atypical objects in genetic as well as non-genetics variables. Identifying significant outliers is an essential and challenging issue for imaging genetics and multiple source…
VEGN uses graph neural networks to predict disease-causing mutations from genetic variants.
problem Identifying disease-causing mutations from millions of genetic variants.
method VEGN employs a graph neural network on a heterogeneous graph of genes and variants, learning gene-gene interactions.
result VEGN outperforms existing state-of-the-art models in variant effect prediction.
EB-VAE combines tumor growth and dropout data for personalized treatment response modeling.
problem Challenges in integrating longitudinal tumor measurements, dropout information, and genetic covariates.
method Extended EB-VAE framework to jointly model longitudinal and time-to-event data, incorporating dropout hazard and genetic covariates.
result Hybrid decoder formulation yields consistent treatment-effect parameters and prior predictive performance comparable to neural decoder.
New method uses DNN for genetic variant identification, controlling randomness and improving interpretability.
problem Challenges in interpreting deep neural networks for genetic variant identification.
method Interpretable neural network model with controlled variable selection using ensembling, knockoffs, and de-randomization.
result The proposed method leads to more discoveries compared to conventional methods.
Statistical Inference for Maximin Effects: Identifying Stable Associations across Multiple Studiesstat.ME
The paper develops methods to identify stable associations across multiple studies.
problem Identifying stable associations across multiple studies with possible distributional shifts.
method Modeling heterogeneous multi-source data with multiple high-dimensional regressions and devising a novel sampling method for valid confidence intervals of maximin effects.
result Significant maximin effects indicate stable associations that can be generalized to target populations.
Deep neural network learning can be formulated as a non-convex optimization problem. Existing optimization algorithms, e.g., Adam, can learn the models fast, but may get stuck in local optima easily. In this paper, we introduce a novel optimization algorithm, namely GADAM (Genetic-Evolutionary Adam). GADAM learns deep …
Enhances genetic programming for stock alpha discovery with warm start and structural constraints.
problem Overwhelming search space and computational burden in traditional genetic programming for alpha factor discovery.
method Proposes a new GP framework with warm start and structural constraints to enhance search performance and interpretability.
result Superior out-of-sample prediction results and higher portfolio returns compared to benchmarks.
New algorithm reconstructs genealogies from genetic data.
problem Reconstructing genealogies from genetic data.
method Iterative algorithm {\sc Rec-Gen} for pedigrees from a generative model.
result Accurate reconstruction of a large fraction of pedigrees with low sample complexity.
In statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been proposed to incorporate additive genetic effects into models for prediction or …
New KNN test improves association analysis of high-dimensional sequencing data.
problem Challenges in using neural networks for high-dimensional sequencing data analysis.
method Kernel-based neural network (KNN) test for complex association analysis.
result KNN test outperforms SKAT in detecting non-linear and interaction effects.
In this paper, we propose a framework for automatic classification of patients from multimodal genetic and brain imaging data by optimally combining them. Additive models with unadapted penalties (such as the classical group lasso penalty or -multiple kernel learning) treat all modalities in the same manner and ca…
Networks of coupled dynamical systems provide a powerful way to model systems with enormously complex dynamics, such as the human brain. Control of synchronization in such networked systems has far reaching applications in many domains, including engineering and medicine. In this paper, we formulate the synchronization…
This study introduces a new GAS blending ensemble model for Bitcoin price prediction.
problem Predicting Bitcoin price fluctuations in the cryptocurrency market.
method Integrates advanced ensemble learning methods, feature selection algorithms, and sentiment analysis.
result The GAS model demonstrates excellent performance in daily Bitcoin trend prediction.
Study investigates how preprocessing, feature selection, and model selection affect performance on imbalanced genetic data.
problem Challenges in using machine learning on imbalanced genetic datasets.
method Comparative analysis of data preprocessing, feature selection techniques, and machine learning models on imbalanced genetic data.
result Class-imbalanced target variables and skewed predictors have little to no impact on classification performance.
Extracting Epistatic Interactions in Type 2 Diabetes Genome-Wide Data Using Stacked Autoencodercs.LG
2 Diabetes is a leading worldwide public health concern, and its increasing prevalence has significant health and economic importance in all nations. The condition is a multifactorial disorder with a complex aetiology. The genetic determinants remain largely elusive, with only a handful of identified candidate genes. G…
We propose a non-parametric regression methodology, Random Forests on Distance Matrices (RFDM), for detecting genetic variants associated to quantitative phenotypes representing the human brain's structure or function, and obtained using neuroimaging techniques. RFDM, which is an extension of decision forests, requires…
A Sparse Graph-Structured Lasso Mixed Model for Genetic Association with Confounding Correctioncs.LG
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the complex structure of genotypic and phenotypic data. For example, geneticists hav…
New hierarchical model improves on standard practice for high-dimensional data.
problem Poor statistical performance in high-dimensional hierarchical models.
method Model effects as exchangeable across covariates and correlated across datasets.
result Empirical Bayes estimator outperforms classic approach in high-dimensional settings.
Semi-supervised GAN creates synthetic genetic data for disease prediction.
problem Expensive and time-consuming to build large labeled genetic databases.
method Semi-supervised Genetic Generative Adversarial Network (gGAN).
result Model achieved satisfactory results with real genetic data.
New methods improve genetic studies of complex diseases.
problem Improving genetic studies of complex diseases using high-dimensional clinical data.
method Evaluation of unsupervised disentangled representation learning methods (autoencoders, VAE, beta-VAE, FactorVAE) for genetic association studies.
result FactorVAEs and beta-VAEs outperform standard VAEs and non-variational autoencoders in genetic studies of asthma and COPD.
A New Statistical Framework for Genetic Pleiotropic Analysis of High Dimensional Phenotype Datastat.ML
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome these limitations, we …
Neural network feature optimization for causal inference.
problem Estimating heterogeneous treatment effects from data.
method Genetic algorithm optimization of intermediate neural network layers for feature representations.
result Retains useful features for outcome prediction even if related to treatment assignment.
Deep learning and genetic algorithms speed up cosmological Bayesian inference.
problem Substantial computational demands in Bayesian inference for cosmological parameter estimation.
method Deep learning using feedforward neural networks to approximate likelihood functions dynamically, optimized with genetic algorithms.
result Significant speed-up in Bayesian inference process for cosmological models and datasets.
New method estimates stochastic intervention effects in decision-making domains.
problem Current causal inference methods are limited to deterministic treatment, unable to handle stochastic policies.
method Developed a new stochastic propensity score and stochastic intervention effect estimator (SIE) with a customized genetic algorithm (Ge-SIO).
result Empirical study shows significant performance improvement over state-of-the-art baselines.
The objective of this paper is to define an effective strategy for building an ensemble of Genetic Programming (GP) models. Ensemble methods are widely used in machine learning due to their features: they average out biases, they reduce the variance and they usually generalize better than single models. Despite these a…
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
problem Lack of methods to model pleiotropy in multi-phenotype GWAS.
method Bayesian inference model using summary statistics, fast computation, and biologically informed priors.
result Demonstrates utility in metabolite GWAS with interpretable pathway-level inference.
Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. A non-parametric Bayesian approach in the form o…
Common complex diseases are likely influenced by the interplay of hundreds, or even thousands, of genetic variants. Converging evidence shows that genetic variants with low marginal effects (LME) play an important role in disease development. Despite their potential significance, discovering LME genetic variants and as…
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or on a dense grid and referred to as function-valued traits. Both physiological a…
Novel tests for genetic independence in high-dimensional data.
problem Testing independence in genetics studies with many variables.
method Defining premetric structures on genetic data support spaces.
result Solid theoretical framework and computationally-efficient implementations.
Selective deconfounding improves ATE estimation with less data.
problem Estimating ATE with unobserved confounders using limited data.
method Combining confounded and deconfounded observational data for ATE estimation.
result Selective deconfounding can significantly reduce the amount of deconfounded data needed.
Paper proposes a hybrid AI method to optimize pandemic actions.
problem Optimizing government actions to balance public health and economy.
method Combines Deep Q-Learning and Genetic Algorithms for optimal sequences of actions.
result Deep Q-Learning outperforms Genetic Algorithms in optimizing action sequences.
Bayesian method selects important covariates in modal regression.
problem Bayesian modal regression with heavy-tailed responses.
method Expectation-maximization algorithm for parameter estimation; test statistic for variable selection.
result Efficacy of the proposed method in identifying important covariates.
New method resolves time order in genetic mutation models.
problem Underspecification in modeling genetic mutation time evolution.
method Continuous-time Markov chains with additional independent items.
result Additional items help determine time order and resolve underspecification.
We introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and Centrifuge on datasets obtained from several sequencing technologies, in which dataset s…
Empirical Bayes Rebiasingstat.ME
We rebias estimates to improve interval calibration and prediction accuracy.
problem Constructing accurate intervals for noisy and biased estimates.
method Empirical Bayes rebiasing strategy that learns bias distribution from data.
result Substantial precision gains in prediction-powered inference.
Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance (KDC). KMR is a semiparametric regression frameworks that models the covariate ef…
Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self tran…